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Blanco P, Hipólito A, García-Pastor L, Trigo da Roza F, Toribio-Celestino L, Ortega A, Vergara E, San Millán Á, Escudero J. Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons. Nucleic Acids Res 2024; 52:2961-2976. [PMID: 38214222 PMCID: PMC11014356 DOI: 10.1093/nar/gkad1252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encode promoterless genes, whose expression relies on the platform-associated Pc promoter, with the cassette array functioning as an operon-like structure regulated by the distance to the Pc. This is relevant in large sedentary chromosomal integrons (SCIs) carrying hundreds of ICs, like those in Vibrio species. We selected 29 gene-less cassettes in four Vibrio SCIs, and explored whether their function could be related to the transcription regulation of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Additionally, we identified the transcription start sites of gene-less ICs through 5'-RACE. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Furthermore, one cassette with an antisense promoter can reduce trimethoprim resistance when cloned downstream. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in SCIs and their clinical importance if captured by mobile integrons.
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Affiliation(s)
- Paula Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
| | - Alba Cristina Ortega
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid 28222, Spain
| | - José Antonio Escudero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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Qi Q, Ghaly TM, Rajabal V, Gillings MR, Tetu SG. Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR. J Antimicrob Chemother 2024; 79:100-111. [PMID: 37962091 DOI: 10.1093/jac/dkad353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVES Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution. METHODS We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host. RESULTS Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli. CONCLUSIONS Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Vaheesan Rajabal
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
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Tansirichaiya S, Winje E, Wigand J, Al-Haroni M. Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome. BMC Oral Health 2022; 22:210. [PMID: 35624467 PMCID: PMC9137128 DOI: 10.1186/s12903-022-02209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
The human oral cavity is one of the hotspots harboring multiple mobile genetic elements (MGEs), which are segments of DNA that can move either within bacterial genomes or between bacterial cells that can facilitate the spreading of genetic materials, including antimicrobial resistance genes. It is, therefore, important to investigate genes associated with the MGEs as they have a high probability of dissemination within the bacterial population under selective pressure from human activities. As one-third of oral bacteria are not yet culturable in the laboratory condition, therefore, in this work, it is aimed to detect and identify the genetic contexts of MGEs in the oral cavity through an inverse PCR (IPCR)-based approach on the oral metagenomic. The human oral metagenome was extracted from saliva samples collected from healthy individuals in Tromsø, Norway. The extracted DNA was partially digested with the HindIII restriction enzyme and self-circularized by ligation. DNA primers targeting each MGE were designed to amplify outwards from the MGEs and used for the IPCR on the circularized DNA products. The IPCR amplicons were cloned into a pCR-XL-2-TOP vector, screened, and sequenced. Out of 40 IPCR amplicons, we confirmed and verified the genetic contexts of 11 samples amplified with primers targeting integron gene cassettes (GCs), IS431 composite transposons, and Tn916 conjugative transposons (tet(M) and xis-int). Novel integron GCs, MGEs, and variants of Tn916 conjugative transposons were identified, which is the first report using the IPCR technique to detect the genetic contexts of MGEs in the oral metagenomic DNA.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway
| | - Endre Winje
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Johannes Wigand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.
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Fonseca ÉL, Vicente AC. Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation. Microorganisms 2022; 10:microorganisms10020224. [PMID: 35208680 PMCID: PMC8876359 DOI: 10.3390/microorganisms10020224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022] Open
Abstract
Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up-to-date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well-balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.
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Ghaly TM, Gillings MR, Penesyan A, Qi Q, Rajabal V, Tetu SG. The Natural History of Integrons. Microorganisms 2021; 9:2212. [PMID: 34835338 PMCID: PMC8618304 DOI: 10.3390/microorganisms9112212] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022] Open
Abstract
Integrons were first identified because of their central role in assembling and disseminating antibiotic resistance genes in commensal and pathogenic bacteria. However, these clinically relevant integrons represent only a small proportion of integron diversity. Integrons are now known to be ancient genetic elements that are hotspots for genomic diversity, helping to generate adaptive phenotypes. This perspective examines the diversity, functions, and activities of integrons within both natural and clinical environments. We show how the fundamental properties of integrons exquisitely pre-adapted them to respond to the selection pressures imposed by the human use of antimicrobial compounds. We then follow the extraordinary increase in abundance of one class of integrons (class 1) that has resulted from its acquisition by multiple mobile genetic elements, and subsequent colonisation of diverse bacterial species, and a wide range of animal hosts. Consequently, this class of integrons has become a significant pollutant in its own right, to the extent that it can now be detected in most ecosystems. As human activities continue to drive environmental instability, integrons will likely continue to play key roles in bacterial adaptation in both natural and clinical settings. Understanding the ecological and evolutionary dynamics of integrons can help us predict and shape these outcomes that have direct relevance to human and ecosystem health.
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Affiliation(s)
- Timothy M. Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
| | - Anahit Penesyan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Qin Qi
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
| | - Vaheesan Rajabal
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
| | - Sasha G. Tetu
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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